X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=f973fbb0dc7ae3173d566c890ec97a0955bcbca8;hb=e30c8f0736f711e2dc7c32680ac57a28c77d567d;hp=e3282d8e37d09403c1f730e1df4f99813a85bcbb;hpb=09feea69607bcbc761c50a7911272f0499ee57e9;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index e3282d8..f973fbb 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -119,8 +119,8 @@ public class SequenceFetcher
                                               new Insets(0, 4, 0, 0), 1, 0));
     this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
                                                , GridBagConstraints.CENTER,
-                                               GridBagConstraints.HORIZONTAL,
-                                               new Insets(0, 0, 0, 6), 200, 1));
+                                               GridBagConstraints.NONE,
+                                               new Insets(0, 0, 0, 6), 211, 1));
   }
 
   JComboBox database = new JComboBox();
@@ -183,16 +183,26 @@ public class SequenceFetcher
     else if (database.getSelectedItem().equals("EMBL")
              || database.getSelectedItem().equals("EMBLCDS"))
     {
-      EBIFetchClient dbFetch = new EBIFetchClient();
-      String[] reply = dbFetch.fetchData(
-          database.getSelectedItem().toString().toLowerCase(
-          ) + ":" + textfield.getText(),
-          "fasta", "raw");
+      StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
+      while(st.hasMoreTokens())
+      {
+        EBIFetchClient dbFetch = new EBIFetchClient();
+
+        String[] reply = dbFetch.fetchData(
+            database.getSelectedItem().toString().toLowerCase(
+            ) + ":" + st.nextToken(),
+            "fasta", "raw");
+//
+        if (reply != null)
+        {
+          for (int i = 0; i < reply.length; i++)
+            result.append(reply[i] + "\n");
+        }
+      }
 
-      if(reply!=null)
+      if(result!=null)
       {
-        for (int i = 0; i < reply.length; i++)
-          result.append(reply[i] + "\n");
+        System.out.println(result.toString());
 
         parseResult(result.toString(), null);
       }
@@ -239,6 +249,7 @@ public class SequenceFetcher
   {
     EBIFetchClient ebi = new EBIFetchClient();
     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
+
     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
     Vector entries = sff.getUniprotEntries(file);
 
@@ -249,7 +260,8 @@ public class SequenceFetcher
       while (en.hasMoreElements())
       {
         UniprotEntry entry = (UniprotEntry) en.nextElement();
-        StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");
+
+        StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
         Enumeration en2 = entry.getAccession().elements();
         while (en2.hasMoreElements())
         {
@@ -263,8 +275,10 @@ public class SequenceFetcher
           name.append(en2.nextElement());
         }
 
-        if (entry.getProteinName() != null)
-          name.append(" " + entry.getProteinName().elementAt(0));
+        if (entry.getProtein() != null)
+        {
+           name.append(" " + entry.getProtein().getName().elementAt(0));
+        }
 
         result.append(name + "\n" + entry.getUniprotSequence().getContent() +
                       "\n");
@@ -288,10 +302,15 @@ public class SequenceFetcher
         }
 
         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
-        e = entry.getFeature().elements();
-        while(e.hasMoreElements())
+        if (entry.getFeature() != null)
         {
-          sequence[i].getDatasetSequence().addSequenceFeature((SequenceFeature)e.nextElement());
+          e = entry.getFeature().elements();
+          while (e.hasMoreElements())
+          {
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
+            sf.setFeatureGroup("Uniprot");
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );
+          }
         }
       }
     }
@@ -341,7 +360,7 @@ public class SequenceFetcher
 
   SequenceI[] parseResult(String result, String title)
   {
-    String format = IdentifyFile.Identify(result, "Paste");
+    String format = new IdentifyFile().Identify(result, "Paste");
     SequenceI[] sequences = null;
 
     if (FormatAdapter.formats.contains(format))
@@ -364,6 +383,12 @@ public class SequenceFetcher
                                    AlignFrame.NEW_WINDOW_WIDTH,
                                    AlignFrame.NEW_WINDOW_HEIGHT);
           af.statusBar.setText("Successfully pasted alignment file");
+          if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+          {
+            af.wrapMenuItem.setSelected(true);
+            af.wrapMenuItem_actionPerformed(null);
+          }
+
           try
           {
             af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
@@ -422,7 +447,7 @@ public class SequenceFetcher
 
               // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
               // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
-              DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);
+              DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",pdbid);
               sequences[i].getDatasetSequence().addDBRef(dbentry);
             }
             else
@@ -451,13 +476,18 @@ public class SequenceFetcher
 
   }
 
-  void showErrorMessage(String error)
+  void showErrorMessage(final String error)
   {
     resetDialog();
-    JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                          error, "Error Retrieving Data",
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              error, "Error Retrieving Data",
                                           JOptionPane.WARNING_MESSAGE);
-    return;
+      }
+    });
   }
 }